E-value and similarity distribution of unigenes with annotation to Nr (NCBI non-redundant protein sequences) database.

<p>(A) E-value distribution of annotated unigenes; (B) Similarity distribution of annotated unigenes.</p

KOG (euKaryotic Ortholog Groups) classification of putative proteins for the mantle transcriptome of <i>P</i>. <i>yessoensis</i>.

<p>KOG (euKaryotic Ortholog Groups) classification of putative proteins for the mantle transcriptome of <i>P</i>. <i>yessoensis</i>.</p

Characterization of the Mantle Transcriptome of Yesso Scallop (<i>Patinopecten yessoensis</i>): Identification of Genes Potentially Involved in Biomineralization and Pigmentation

<div><p>The Yesso scallop <i>Patinopecten yessoensis</i> is an economically important marine bivalve species in aquaculture and fishery in Asian countries. However, limited genomic resources are available for this scallop, which hampers investigations into molecular mechanisms underlying their unique biological characteristics, such as shell formation and pigmentation. Mantle is the special tissue of <i>P</i>. <i>yessoensis</i> that secretes biomineralization proteins inducing shell deposition as well as pigmentation on the shells. However, a current deficiency of transcriptome information limits insight into mechanisms of shell formation and pigmentation in this species. In this study, the transcriptome of the mantle of <i>P</i>. <i>yessoensis</i> was deeply sequenced and characterized using Illumina RNA-seq technology. A total of 86,521 unique transcripts are assembled from 55,884,122 reads that passed quality filters, and annotated, using Gene Ontology classification. A total of 259 pathways are identified in the mantle transcriptome, including the calcium signaling and melanogenesis pathways. A total of 237 unigenes that are homologous to 102 reported biomineralization genes are identified, and 121 unigenes that are homologous to 93 known proteins related to melanin biosynthesis are found. Twenty-three annotated unigenes, which are mainly homologous to calmodulin and related proteins, Ca2+/calmodulin-dependent protein kinase, adenylate/guanylate cyclase, and tyrosinase family are potentially involved in both biomineralization and melanin biosynthesis. It is suggested that these genes are probably not limited in function to induce shell deposition by calcium metabolism, but may also be involved in pigmentation of the shells of the scallop. This potentially supports the idea that there might be a link between calcium metabolism and melanin biosynthesis, which was previously found in vertebrates. The findings presented here will notably advance the understanding of the sophisticated processes of shell formation as well as shell pigmentation in <i>P</i>. <i>yessoensis</i> and other bivalve species, and also provide new evidence on gene expression for the understanding of pigmentation and biomineralization not only in invertebrates but also probably in vertebrates.</p></div

The shell picture for Yesso scallop <i>Patinopecten yessoensis</i>.

<p>The predominant color of the left valve is dark brown, while the absence of pigmentation occurs on the right valve.</p

KEGG (Kyoto Encyclopedia of Genes and Genomes) assignment of unigenes in the mantle transcriptome of <i>P. yessoensis</i>.

<p>A, Cellular Processes; B, Enviromental Information Processing; C, Genetic Information Processing; D, Metabolism; E, Organismal Systems.</p

GO (Gene Ontology) categorization (Biological process, Cellular component and Molecular function) of unigenes in the mantle transcriptome of <i>P</i>. <i>yessoensis</i>.

<p>Each annotated sequence is assigned at least one GO term.</p

Sequence length distribution of transcripts and unigenes assembled from Illumina reads for the mantle transcriptome of <i>P</i>. <i>yessoensis</i>.

<p>The x-axis indicates length interval of transcripts and unigenes, and the y-axis indicates number of transcripts and unigenes for each size.</p

The unigenes related to both biomineralization and melanin biosynthesis in the mantle transcriptome of <i>P</i>. <i>yessoensis</i>.

<p>The unigenes related to both biomineralization and melanin biosynthesis in the mantle transcriptome of <i>P</i>. <i>yessoensis</i>.</p

Statistics of de novo assembly for the mantle transcriptome of <i>P</i>. <i>yessoensis</i>.

<p>Statistics of de novo assembly for the mantle transcriptome of <i>P</i>. <i>yessoensis</i>.</p

The quantification of tyrosinase activities and protein level (ELISA test) in the mantle of Red and White scallops.

<p>The quantification of tyrosinase activities and protein level (ELISA test) in the mantle of Red and White scallops.</p